User: nac

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nac280
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Posts by nac

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Answer: A: TEQC package very slow
... HI, This is the error message produced at the myreadpair<-reads2pairs(myread) stage after it running for 7 hours: > readpairs4_2_PigS<-reads2pairs(reads4_2_PigS) [1] "there were 1453928 reads found without matching second read, or whose second read matches to a different chromosome" Err ...
written 5.4 years ago by nac280
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TEQC package very slow
... HI, I am analysing coverage data using TEQC package from bioC for quality assessment of target enrichment experiment . I am using a computer cluster farm to do the analysis and asked for large memory to be allocated, my bam files are 11 Gb in size and it seems that the analysis is taking very long, ...
coverage teqc written 5.4 years ago by nac280
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TEQC package isssue with chromosome format
... Hi, I would like to analyse the coverage of my Bam files using TEQC package which have been aligned on a reference with the following format chr number (1-19, X, Y ), start (integrer), end (integrer) the chromosomes are not with the prefixe chr. When I try to create the target file with the Nochr n ...
coverage written 5.5 years ago by nac280
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TEQC see all the reads with a given coverage
... HI all, I am using TEQC to have a look at coverage on my custom pull down sequencing #bam file reads<-get.reads("./13.bam",filetype="bam") #target file from which the baits has been designed: targets<-get.targets("target.txt", chrcol=1,startcol=2,endcol=3, zerobased=F, sep="\t",skip=0) readp ...
coverage teqc written 5.5 years ago by nac280
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Comment: C: extract data from RangedData table (IRange TEQC packages)
... On 19/04/12 16:43, Ivan Gregoretti wrote: > write.table(as.data.frame(targets)[,c(1,2,3)],file="./output.bed", > quote=FALSE, sep="\t", row.names=FALSE, col.names=FALSE) works brilliantly thanks :) -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity reg ...
written 5.6 years ago by nac280
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extract data from RangedData table (IRange TEQC packages)
... Hi, I would like to extract a txt file of a RangedData table I have created with TEQC package using the get.targets function and a bed target file "file" as an input: > targets<-get.targets("file", chrcol=1,startcol=2,endcol=3, zerobased=F, sep="\t",skip=0) [1] "read 1243 target regions in ...
teqc written 5.6 years ago by nac280 • updated 5.6 years ago by Michael Lawrence9.8k
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Checking RNAseq DESeq pipeline
... Hi all, I have done an differential expression analysis using DESeq on a set of data and got a lot of differential expressed genes at the end. I would like people to check the code and the assumptions I made. A-Samples I am analysing 6 samples in total from 3 different cell types (E, S and H), S1 ...
sequencing process deseq written 5.7 years ago by nac280 • updated 5.7 years ago by Wolfgang Huber13k
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package to count read prior to DESeq?
... Hi, Is there a package to create a count table from bam files, which gives an output compatible with DESeq analysis? thanks Nat -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England ...
deseq written 5.8 years ago by nac280 • updated 5.8 years ago by Wei Shi2.7k
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CNTools error message
... Hi, I am analysing CGH data using DNAcopy to create segmented data and CNTools package to reduce the segments by genes. No issue there. #I created the segmentList object using segment function of DNAcopy segmentList<-segment(smooth.CNA_order1.5,undo.splits="sdundo",undo.SD= 1.5,verbose=1) mySegl ...
cgh probe dnacopy written 5.8 years ago by nac280 • updated 5.8 years ago by Martin Morgan ♦♦ 20k
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Comment: C: questions on cghMCR package
... HI, Is anybody using cghMCR in the R/BioC community please? I have been trying to get some of my questions answered and didn't get lucky, maybe this package is not maintained anymore.. If not Do you know any other package that could identify Minimal common genomic regions of interests based on segme ...
written 5.8 years ago by nac280

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